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- PDB-5lt5: Carboxysome shell protein CcmP from Synechococcus elongatus PCC 7942 -

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Basic information

Entry
Database: PDB / ID: 5lt5
TitleCarboxysome shell protein CcmP from Synechococcus elongatus PCC 7942
ComponentsCcmP
KeywordsTRANSPORT PROTEIN / Carboxysome Shell protein BMC domain Gated transport
Function / homology
Function and homology information


structural constituent of carboxysome shell / carboxysome / carbon fixation / photosynthesis
Similarity search - Function
Bacterial microcompartment (BMC) circularly permuted domain / Bacterial microcompartment (BMC) circularly permuted domain profile. / BMC (bacterial microcompartment) domain / Bacterial microcompartment domain / BMC / CcmK-like superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Carboxysome shell protein CcmP
Similarity search - Component
Biological speciesSynechococcus elongatus PCC 7942 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.45 Å
AuthorsLarsson, A.M. / Hasse, D. / Valegard, K. / Andersson, I.
Funding support Sweden, 4items
OrganizationGrant numberCountry
Swedish Research Council Sweden
Knut and Alice Wallenberg Foundation Sweden
European Research Council Sweden
Rontgen-Angstrom Cluster Sweden
CitationJournal: J. Exp. Bot. / Year: 2017
Title: Crystal structures of beta-carboxysome shell protein CcmP: ligand binding correlates with the closed or open central pore.
Authors: Larsson, A.M. / Hasse, D. / Valegard, K. / Andersson, I.
History
DepositionSep 6, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CcmP
B: CcmP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7635
Polymers48,5432
Non-polymers2203
Water5,855325
1
A: CcmP
B: CcmP
hetero molecules

A: CcmP
B: CcmP
hetero molecules

A: CcmP
B: CcmP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,28915
Polymers145,6306
Non-polymers6599
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-z,x+1/2,-y+1/21
crystal symmetry operation11_455y-1/2,-z+1/2,-x1
Buried area20570 Å2
ΔGint-98 kcal/mol
Surface area38950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.154, 107.154, 107.154
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213

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Components

#1: Protein CcmP


Mass: 24271.646 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus elongatus PCC 7942 (bacteria)
Gene: Synpcc7942_0520 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): AI / References: UniProt: Q31QW7
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 325 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 41.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20 mM BIS-tris propane, 50 mM NaCl, 10 mM glycerol, 0.2 M Li sulphate, 0.1 mM Tris-HCl pH 7.5 and 5% w/v PEG 4000, 50 mM RuBP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97239 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97239 Å / Relative weight: 1
ReflectionResolution: 1.45→47.92 Å / Num. obs: 72625 / % possible obs: 100 % / Redundancy: 9.9 % / Biso Wilson estimate: 19.17 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.058 / Net I/σ(I): 21.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.45-1.479.60.8930.7791100
7.94-47.929.50.0281199.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.1.29data scaling
BUSTER-TNT1.10.0refinement
PDB_EXTRACT3.2data extraction
XDSNovember 11, 2013data reduction
PHASER2.5.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HT5

4ht5


Resolution: 1.45→47.92 Å / Cor.coef. Fo:Fc: 0.9615 / Cor.coef. Fo:Fc free: 0.9536 / SU R Cruickshank DPI: 0.059 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.061 / SU Rfree Blow DPI: 0.06 / SU Rfree Cruickshank DPI: 0.059
RfactorNum. reflection% reflectionSelection details
Rfree0.1836 3659 5.04 %RANDOM
Rwork0.165 ---
obs0.166 72565 99.97 %-
Displacement parametersBiso max: 101.51 Å2 / Biso mean: 21.32 Å2 / Biso min: 11.07 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.145 Å
Refinement stepCycle: final / Resolution: 1.45→47.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3130 0 13 325 3468
Biso mean--26.09 33.14 -
Num. residues----409
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1204SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes85HARMONIC2
X-RAY DIFFRACTIONt_gen_planes502HARMONIC5
X-RAY DIFFRACTIONt_it3311HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion435SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4324SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3311HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4498HARMONIC21.05
X-RAY DIFFRACTIONt_omega_torsion4.22
X-RAY DIFFRACTIONt_other_torsion14.98
LS refinement shellResolution: 1.45→1.49 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2167 296 5.55 %
Rwork0.1909 5035 -
all0.1923 5331 -
obs--99.97 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.51650.15870.43820.3380.16120.92180.0603-0.0591-0.07090.0577-0.0121-0.00550.1378-0.0925-0.0482-0.0108-0.0049-0.0003-0.03880.0048-0.01176.165432.15292.7687
20.5518-0.17010.27490.511-0.07230.40320.00870.0855-0.0171-0.08720.0032-0.0395-0.02520.058-0.0119-0.0107-0.00180.0168-0.0079-0.0118-0.03538.947453.2142-25.9122
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A3 - 206
2X-RAY DIFFRACTION2{ B|* }B2 - 206

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